Bottom Line:
Similar results are also found in simulations that include an external torque to induce over- or unwinding of DNA and RNA.Overwinding of RNA results in more compact conformations with a narrower major groove and consequently reduced helical extension.Overwinding of DNA decreases the size of the minor groove and the resulting positive base pair inclination leads to a slender and more extended helical structure.

Figure 1: (A) Snapshots of undertwisted (left) and overtwisted (right) dsDNA and dsRNA extracted from 1 μs Molecular Dynamics simulations. In case of DNA the overtwisted snapshot indicates a greater extension in the helical (z) axis direction and a smaller diameter compared to the unwound snapshot. For RNA the overtwisted snapshot shows a reduced extension in the z-direction, a more closed major groove and also a reduced diameter compared to an unwound snapshot. (B) Root mean square deviation (RMSD) of all heavy atoms of the central 10 base pairs with respect to standard B-form DNA (left plot) and standard A-form RNA (right plot) sampled during the entire data gathering simulations.

Mentions:
The 1 μs MD simulations of DNA and RNA duplex molecules resulted in sampled conformations that stayed overall close to the B-form or A-from starting structures, respectively (Figure 1). Slightly larger root mean square deviation (RMSD) of the 10 central base pairs with respect to the start structures was observed for dsDNA compared to dsRNA (Figure 1). During the simulations a range of conformations with varying overall twist and extension in the direction of the helical axis were sampled (illustrated by snapshots observed during the simulations, Figure 1). To avoid any influence of the sterically less restricted terminal base pairs the analysis of helical parameters was limited to the 10 central base pairs. Note, that the molecules contain each sequence of possible base pair steps at least once to approximately mimic a random sequence. Neglecting details of the nucleic acid backbone and assuming near rigid geometry of the nucleo-bases allows the description of the placement of each base pair in a duplex structure along a central helical axis by the helical parameters x-displacement (x-disp), y-displacement (y-disp), helical rise, inclination, tip and helical twist (Figure 2). Alternatively, it is also possible to describe a helical duplex structure with respect to the local base pair step parameters shift, slide, rise, tilt, roll and twist (with respect to a local base pair step) (59,60) (Figure 2). The description is completed by six additional intra-base pair helical parameters that describe the internal geometry of bases within each base pair (59,60). We focus on the base pair axis parameters in particular on the relation of helical rise and helical twist since these are the variables that are manipulated and measured in single molecule experiments that twist and stretch duplex molecules (27). The mean helical twist of the central base pair steps extracted from the simulations was 32.0° for DNA and 31.5° for RNA. Whereas the value for RNA is close to standard A-form RNA twist (∼32°) for DNA it is slightly smaller than the standard B-DNA twist of 36° (59). However, it is close to what has been found as average twist (32.5°) in a systematic MD comparison of all possible 136 DNA tetra-nucleotides embedded in duplex molecules using the same force field (49). The observed fluctuations in helical twist (1.1° for DNA and 0.9° for RNA) and rise (0.11 Å for DNA and 0.15 Å for RNA) are compatible with available experimental data on the twist and stretch modulus of DNA and RNA, respectively.

Figure 1: (A) Snapshots of undertwisted (left) and overtwisted (right) dsDNA and dsRNA extracted from 1 μs Molecular Dynamics simulations. In case of DNA the overtwisted snapshot indicates a greater extension in the helical (z) axis direction and a smaller diameter compared to the unwound snapshot. For RNA the overtwisted snapshot shows a reduced extension in the z-direction, a more closed major groove and also a reduced diameter compared to an unwound snapshot. (B) Root mean square deviation (RMSD) of all heavy atoms of the central 10 base pairs with respect to standard B-form DNA (left plot) and standard A-form RNA (right plot) sampled during the entire data gathering simulations.

Mentions:
The 1 μs MD simulations of DNA and RNA duplex molecules resulted in sampled conformations that stayed overall close to the B-form or A-from starting structures, respectively (Figure 1). Slightly larger root mean square deviation (RMSD) of the 10 central base pairs with respect to the start structures was observed for dsDNA compared to dsRNA (Figure 1). During the simulations a range of conformations with varying overall twist and extension in the direction of the helical axis were sampled (illustrated by snapshots observed during the simulations, Figure 1). To avoid any influence of the sterically less restricted terminal base pairs the analysis of helical parameters was limited to the 10 central base pairs. Note, that the molecules contain each sequence of possible base pair steps at least once to approximately mimic a random sequence. Neglecting details of the nucleic acid backbone and assuming near rigid geometry of the nucleo-bases allows the description of the placement of each base pair in a duplex structure along a central helical axis by the helical parameters x-displacement (x-disp), y-displacement (y-disp), helical rise, inclination, tip and helical twist (Figure 2). Alternatively, it is also possible to describe a helical duplex structure with respect to the local base pair step parameters shift, slide, rise, tilt, roll and twist (with respect to a local base pair step) (59,60) (Figure 2). The description is completed by six additional intra-base pair helical parameters that describe the internal geometry of bases within each base pair (59,60). We focus on the base pair axis parameters in particular on the relation of helical rise and helical twist since these are the variables that are manipulated and measured in single molecule experiments that twist and stretch duplex molecules (27). The mean helical twist of the central base pair steps extracted from the simulations was 32.0° for DNA and 31.5° for RNA. Whereas the value for RNA is close to standard A-form RNA twist (∼32°) for DNA it is slightly smaller than the standard B-DNA twist of 36° (59). However, it is close to what has been found as average twist (32.5°) in a systematic MD comparison of all possible 136 DNA tetra-nucleotides embedded in duplex molecules using the same force field (49). The observed fluctuations in helical twist (1.1° for DNA and 0.9° for RNA) and rise (0.11 Å for DNA and 0.15 Å for RNA) are compatible with available experimental data on the twist and stretch modulus of DNA and RNA, respectively.

Bottom Line:
Similar results are also found in simulations that include an external torque to induce over- or unwinding of DNA and RNA.Overwinding of RNA results in more compact conformations with a narrower major groove and consequently reduced helical extension.Overwinding of DNA decreases the size of the minor groove and the resulting positive base pair inclination leads to a slender and more extended helical structure.